Correlation between gene mutation status and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 26 genes and 10 molecular subtypes across 282 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • NF2 mutation correlated to 'METHLYATION_CNMF'.

  • MET mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NEFH mutation correlated to 'CN_CNMF'.

  • KRAS mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • SMARCB1 mutation correlated to 'METHLYATION_CNMF'.

  • TP53 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • PBRM1 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • SAV1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 26 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 19 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
SETD2 16 (6%) 266 0.177
(0.661) 		1e-05
(0.0026) 		0.0826
(0.482) 		0.0597
(0.458) 		0.0161
(0.234) 		0.00387
(0.118) 		0.0482
(0.418) 		0.0041
(0.118) 		0.77
(1.00) 		0.86
(1.00)
MET 21 (7%) 261 0.629
(0.998) 		0.00039
(0.0253) 		0.0834
(0.482) 		0.061
(0.458) 		0.00974
(0.185) 		0.00092
(0.0478) 		0.0302
(0.357) 		0.446
(0.913) 		0.85
(1.00) 		0.0162
(0.234)
SAV1 6 (2%) 276 0.0387
(0.387) 		0.00584
(0.138) 		0.376
(0.853) 		0.384
(0.853) 		0.00029
(0.0251) 		0.00019
(0.0247) 		0.296
(0.824) 		0.157
(0.648) 		0.329
(0.824) 		0.388
(0.853)
KRAS 5 (2%) 277 0.306
(0.824) 		0.00996
(0.185) 		0.486
(0.927) 		0.0178
(0.244) 		0.829
(1.00) 		0.524
(0.959) 		0.373
(0.853) 		0.566
(0.987)
PBRM1 11 (4%) 271 0.838
(1.00) 		0.00227
(0.0843) 		0.223
(0.755) 		0.17
(0.66) 		0.0797
(0.482) 		0.0732
(0.458) 		0.041
(0.395) 		0.00186
(0.0806) 		0.365
(0.853) 		0.38
(0.853)
NF2 10 (4%) 272 0.236
(0.786) 		0.00498
(0.129) 		0.68
(1.00) 		0.765
(1.00) 		0.178
(0.661) 		0.112
(0.551) 		0.79
(1.00) 		0.851
(1.00) 		0.872
(1.00) 		0.745
(1.00)
NEFH 6 (2%) 276 0.00932
(0.185) 		0.136
(0.591) 		0.564
(0.987) 		0.461
(0.916) 		0.325
(0.824) 		0.638
(0.998) 		0.635
(0.998) 		0.77
(1.00) 		0.222
(0.755) 		0.383
(0.853)
SMARCB1 6 (2%) 276 0.266
(0.824) 		0.014
(0.227) 		1
(1.00) 		0.546
(0.972) 		0.106
(0.551) 		0.143
(0.601) 		0.299
(0.824) 		0.331
(0.824) 		0.036
(0.381) 		0.122
(0.556)
TP53 7 (2%) 275 0.272
(0.824) 		0.0715
(0.458) 		0.267
(0.824) 		1
(1.00) 		0.139
(0.594) 		0.0137
(0.227) 		0.45
(0.913) 		0.722
(1.00) 		0.468
(0.916) 		0.122
(0.556)
ZNF814 9 (3%) 273 0.902
(1.00) 		0.621
(0.998) 		1
(1.00) 		0.641
(0.998) 		0.732
(1.00) 		1
(1.00) 		0.116
(0.551) 		0.293
(0.824) 		1
(1.00) 		0.774
(1.00)
CUL3 10 (4%) 272 0.0464
(0.418) 		0.0662
(0.458) 		0.472
(0.916) 		0.507
(0.938) 		0.217
(0.754) 		0.164
(0.657) 		0.113
(0.551) 		0.187
(0.666) 		0.177
(0.661) 		0.499
(0.934)
PCF11 11 (4%) 271 0.33
(0.824) 		0.316
(0.824) 		0.342
(0.831) 		0.0366
(0.381) 		0.116
(0.551) 		0.323
(0.824) 		0.881
(1.00) 		0.39
(0.853) 		0.774
(1.00) 		0.376
(0.853)
BCLAF1 6 (2%) 276 0.889
(1.00) 		0.403
(0.862) 		0.639
(0.998) 		0.813
(1.00) 		0.849
(1.00) 		0.868
(1.00) 		0.509
(0.938) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PAM 3 (1%) 279 0.781
(1.00) 		0.109
(0.551) 		0.0625
(0.458) 		0.69
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.266
(0.824) 		0.0209
(0.272)
KDM6A 10 (4%) 272 0.444
(0.913) 		0.0679
(0.458) 		1
(1.00) 		0.798
(1.00) 		0.464
(0.916) 		0.288
(0.824) 		0.0858
(0.485) 		0.551
(0.975) 		0.31
(0.824) 		0.589
(0.998)
AR 13 (5%) 269 0.381
(0.853) 		0.336
(0.824) 		1
(1.00) 		0.859
(1.00) 		0.755
(1.00) 		0.241
(0.795) 		0.612
(0.998) 		0.725
(1.00) 		0.608
(0.998) 		0.601
(0.998)
KRTAP4-5 5 (2%) 277 0.724
(1.00) 		0.705
(1.00) 		0.834
(1.00) 		0.27
(0.824) 		0.962
(1.00) 		1
(1.00) 		0.136
(0.591) 		0.74
(1.00) 		0.695
(1.00) 		0.386
(0.853)
BRAF 4 (1%) 278 0.443
(0.913) 		0.66
(1.00) 		1
(1.00) 		0.609
(0.998) 		0.938
(1.00) 		1
(1.00) 		0.428
(0.898) 		0.47
(0.916) 		0.316
(0.824) 		0.129
(0.578)
KIAA0922 5 (2%) 277 0.767
(1.00) 		0.959
(1.00) 		0.281
(0.824) 		0.592
(0.998) 		0.718
(1.00) 		0.615
(0.998) 		0.11
(0.551) 		0.288
(0.824)
KRT2 5 (2%) 277 0.0695
(0.458) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.622
(0.998) 		1
(1.00) 		0.775
(1.00) 		0.739
(1.00) 		0.317
(0.824) 		0.535
(0.972)
ALMS1 8 (3%) 274 0.414
(0.874) 		0.947
(1.00) 		0.896
(1.00) 		0.308
(0.824) 		0.946
(1.00) 		0.792
(1.00) 		0.893
(1.00) 		1
(1.00) 		1
(1.00) 		0.681
(1.00)
GXYLT1 4 (1%) 278 0.274
(0.824) 		0.671
(1.00) 		0.482
(0.927) 		0.468
(0.916) 		1
(1.00) 		1
(1.00) 		0.168
(0.66) 		0.689
(1.00) 		0.542
(0.972) 		0.0293
(0.357)
ATP1B1 7 (2%) 275 0.16
(0.649) 		0.606
(0.998) 		0.852
(1.00) 		0.608
(0.998) 		0.0541
(0.454) 		0.182
(0.662) 		0.202
(0.711) 		0.722
(1.00) 		0.0469
(0.418) 		0.851
(1.00)
PTEN 7 (2%) 275 0.889
(1.00) 		0.183
(0.662) 		1
(1.00) 		0.744
(1.00) 		0.336
(0.824) 		0.405
(0.862) 		0.265
(0.824) 		0.495
(0.932) 		0.869
(1.00) 		0.104
(0.551)
CALCR 3 (1%) 279 1
(1.00) 		0.745
(1.00) 		0.631
(0.998) 		0.884
(1.00) 		0.283
(0.824) 		0.0711
(0.458) 		0.712
(1.00) 		0.488
(0.927) 		0.777
(1.00) 		1
(1.00)
IGSF3 4 (1%) 278 0.542
(0.972) 		0.604
(0.998) 		0.0922
(0.51) 		0.074
(0.458) 		0.373
(0.853) 		0.395
(0.855) 		0.969
(1.00) 		0.0683
(0.458) 		0.0323
(0.365) 		1
(1.00)
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.66

Table S1.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
SETD2 MUTATED 6 1 3 6
SETD2 WILD-TYPE 96 70 45 53
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S2.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
SETD2 MUTATED 0 3 1 1 11 0
SETD2 WILD-TYPE 56 39 57 57 15 27

Figure S1.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0826 (Fisher's exact test), Q value = 0.48

Table S3.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
SETD2 MUTATED 2 4 7
SETD2 WILD-TYPE 73 75 48
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0597 (Fisher's exact test), Q value = 0.46

Table S4.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
SETD2 MUTATED 0 4 3 6
SETD2 WILD-TYPE 39 61 60 36
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
SETD2 MUTATED 0 2 8 0 6
SETD2 WILD-TYPE 32 86 61 31 55

Figure S2.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00387 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
SETD2 MUTATED 13 2 1
SETD2 WILD-TYPE 101 119 45

Figure S3.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.42

Table S7.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
SETD2 MUTATED 1 4 1 6 3 1
SETD2 WILD-TYPE 28 33 63 34 77 31

Figure S4.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0041 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
SETD2 MUTATED 13 1 2
SETD2 WILD-TYPE 103 78 85

Figure S5.  Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
SETD2 MUTATED 5 3 5
SETD2 WILD-TYPE 65 71 69
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
SETD2 MUTATED 6 6 1
SETD2 WILD-TYPE 85 89 31
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.79

Table S11.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
NF2 MUTATED 4 1 4 1
NF2 WILD-TYPE 98 70 44 58
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00498 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
NF2 MUTATED 1 0 0 2 4 2
NF2 WILD-TYPE 55 42 58 56 22 25

Figure S6.  Get High-res Image Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
NF2 MUTATED 4 2 2
NF2 WILD-TYPE 71 77 53
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
NF2 MUTATED 1 2 4 1
NF2 WILD-TYPE 38 63 59 41
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.66

Table S15.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
NF2 MUTATED 2 3 0 1 4
NF2 WILD-TYPE 30 85 69 30 57
'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.55

Table S16.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
NF2 MUTATED 2 4 4
NF2 WILD-TYPE 112 117 42
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
NF2 MUTATED 0 1 3 2 4 0
NF2 WILD-TYPE 29 36 61 38 76 32
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
NF2 MUTATED 4 2 4
NF2 WILD-TYPE 112 77 83
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
NF2 MUTATED 1 2 3
NF2 WILD-TYPE 69 72 71
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
NF2 MUTATED 3 3 0
NF2 WILD-TYPE 88 92 32
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
ZNF814 MUTATED 4 2 2 1
ZNF814 WILD-TYPE 98 69 46 58
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
ZNF814 MUTATED 2 1 3 1 2 0
ZNF814 WILD-TYPE 54 41 55 57 24 27
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
ZNF814 MUTATED 2 3 2
ZNF814 WILD-TYPE 73 76 53
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
ZNF814 MUTATED 0 3 3 1
ZNF814 WILD-TYPE 39 62 60 41
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
ZNF814 MUTATED 0 3 3 0 3
ZNF814 WILD-TYPE 32 85 66 31 58
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
ZNF814 MUTATED 4 4 1
ZNF814 WILD-TYPE 110 117 45
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.55

Table S27.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
ZNF814 MUTATED 0 0 3 4 1 1
ZNF814 WILD-TYPE 29 37 61 36 79 31
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.82

Table S28.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
ZNF814 MUTATED 6 2 1
ZNF814 WILD-TYPE 110 77 86
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
ZNF814 MUTATED 2 3 2
ZNF814 WILD-TYPE 68 71 72
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
ZNF814 MUTATED 3 4 0
ZNF814 WILD-TYPE 88 91 32
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
MET MUTATED 7 8 3 3
MET WILD-TYPE 95 63 45 56
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.025

Table S32.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
MET MUTATED 4 1 13 2 0 0
MET WILD-TYPE 52 41 45 56 26 27

Figure S7.  Get High-res Image Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0834 (Fisher's exact test), Q value = 0.48

Table S33.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
MET MUTATED 8 9 1
MET WILD-TYPE 67 70 54
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.061 (Fisher's exact test), Q value = 0.46

Table S34.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
MET MUTATED 3 9 6 0
MET WILD-TYPE 36 56 57 42
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.18

Table S35.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
MET MUTATED 5 8 1 5 2
MET WILD-TYPE 27 80 68 26 59

Figure S8.  Get High-res Image Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.048

Table S36.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
MET MUTATED 2 17 2
MET WILD-TYPE 112 104 44

Figure S9.  Get High-res Image Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.36

Table S37.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
MET MUTATED 0 0 4 3 8 6
MET WILD-TYPE 29 37 60 37 72 26

Figure S10.  Get High-res Image Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 0.91

Table S38.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
MET MUTATED 8 4 9
MET WILD-TYPE 108 75 78
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
MET MUTATED 4 6 6
MET WILD-TYPE 66 68 68
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.23

Table S40.  Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
MET MUTATED 7 3 6
MET WILD-TYPE 84 92 26

Figure S11.  Get High-res Image Gene #4: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00932 (Fisher's exact test), Q value = 0.18

Table S41.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
NEFH MUTATED 0 1 4 1
NEFH WILD-TYPE 102 70 44 58

Figure S12.  Get High-res Image Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.59

Table S42.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
NEFH MUTATED 2 0 0 4 0 0
NEFH WILD-TYPE 54 42 58 54 26 27
'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.99

Table S43.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
NEFH MUTATED 2 2 0
NEFH WILD-TYPE 73 77 55
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 0.92

Table S44.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
NEFH MUTATED 2 1 1 0
NEFH WILD-TYPE 37 64 62 42
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.82

Table S45.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
NEFH MUTATED 2 2 2 0 0
NEFH WILD-TYPE 30 86 67 31 61
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
NEFH MUTATED 2 4 0
NEFH WILD-TYPE 112 117 46
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
NEFH MUTATED 0 0 3 1 1 1
NEFH WILD-TYPE 29 37 61 39 79 31
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
NEFH MUTATED 3 2 1
NEFH WILD-TYPE 113 77 86
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.75

Table S49.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
NEFH MUTATED 1 3 0
NEFH WILD-TYPE 69 71 74
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.85

Table S50.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
NEFH MUTATED 3 1 0
NEFH WILD-TYPE 88 94 32
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.82

Table S51.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
KRAS MUTATED 3 0 0 2
KRAS WILD-TYPE 99 71 48 57
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00996 (Fisher's exact test), Q value = 0.18

Table S52.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
KRAS MUTATED 0 0 2 0 0 3
KRAS WILD-TYPE 56 42 56 58 26 24

Figure S13.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.93

Table S53.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
KRAS MUTATED 0 2 0 1 2
KRAS WILD-TYPE 32 86 69 30 59
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.24

Table S54.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
KRAS MUTATED 0 2 3
KRAS WILD-TYPE 114 119 43

Figure S14.  Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
KRAS MUTATED 0 0 1 1 3 0
KRAS WILD-TYPE 29 37 63 39 77 32
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.96

Table S56.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
KRAS MUTATED 1 1 3
KRAS WILD-TYPE 115 78 84
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.85

Table S57.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
KRAS MUTATED 0 2 3
KRAS WILD-TYPE 70 72 71
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.99

Table S58.  Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
KRAS MUTATED 1 3 1
KRAS WILD-TYPE 90 92 31
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.42

Table S59.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
CUL3 MUTATED 8 1 0 1
CUL3 WILD-TYPE 94 70 48 58

Figure S15.  Get High-res Image Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0662 (Fisher's exact test), Q value = 0.46

Table S60.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
CUL3 MUTATED 2 2 1 1 4 0
CUL3 WILD-TYPE 54 40 57 57 22 27
'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.92

Table S61.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
CUL3 MUTATED 2 5 1
CUL3 WILD-TYPE 73 74 54
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 0.94

Table S62.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
CUL3 MUTATED 0 4 3 1
CUL3 WILD-TYPE 39 61 60 41
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.75

Table S63.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
CUL3 MUTATED 0 1 5 1 3
CUL3 WILD-TYPE 32 87 64 30 58
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.66

Table S64.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
CUL3 MUTATED 7 2 1
CUL3 WILD-TYPE 107 119 45
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.55

Table S65.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
CUL3 MUTATED 0 3 1 3 1 2
CUL3 WILD-TYPE 29 34 63 37 79 30
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.67

Table S66.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
CUL3 MUTATED 7 1 2
CUL3 WILD-TYPE 109 78 85
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.66

Table S67.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
CUL3 MUTATED 5 1 2
CUL3 WILD-TYPE 65 73 72
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 0.93

Table S68.  Gene #7: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
CUL3 MUTATED 5 2 1
CUL3 WILD-TYPE 86 93 31
'PCF11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.82

Table S69.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
PCF11 MUTATED 5 4 0 1
PCF11 WILD-TYPE 97 67 48 58
'PCF11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.82

Table S70.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
PCF11 MUTATED 3 4 2 1 0 0
PCF11 WILD-TYPE 53 38 56 57 26 27
'PCF11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.83

Table S71.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
PCF11 MUTATED 3 1 3
PCF11 WILD-TYPE 72 78 52
'PCF11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.38

Table S72.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
PCF11 MUTATED 3 0 1 3
PCF11 WILD-TYPE 36 65 62 39

Figure S16.  Get High-res Image Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PCF11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.55

Table S73.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
PCF11 MUTATED 0 3 5 2 0
PCF11 WILD-TYPE 32 85 64 29 61
'PCF11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.82

Table S74.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
PCF11 MUTATED 6 4 0
PCF11 WILD-TYPE 108 117 46
'PCF11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
PCF11 MUTATED 1 2 2 2 4 0
PCF11 WILD-TYPE 28 35 62 38 76 32
'PCF11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.85

Table S76.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
PCF11 MUTATED 7 2 2
PCF11 WILD-TYPE 109 77 85
'PCF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
PCF11 MUTATED 3 2 4
PCF11 WILD-TYPE 67 72 70
'PCF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.85

Table S78.  Gene #8: 'PCF11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
PCF11 MUTATED 3 6 0
PCF11 WILD-TYPE 88 89 32
'BCLAF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S79.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
BCLAF1 MUTATED 2 1 1 2
BCLAF1 WILD-TYPE 100 70 47 57
'BCLAF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.86

Table S80.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
BCLAF1 MUTATED 2 0 0 2 1 1
BCLAF1 WILD-TYPE 54 42 58 56 25 26
'BCLAF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
BCLAF1 MUTATED 2 1 2
BCLAF1 WILD-TYPE 73 78 53
'BCLAF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
BCLAF1 MUTATED 1 2 2 0
BCLAF1 WILD-TYPE 38 63 61 42
'BCLAF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
BCLAF1 MUTATED 0 2 1 1 2
BCLAF1 WILD-TYPE 32 86 68 30 59
'BCLAF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
BCLAF1 MUTATED 3 2 1
BCLAF1 WILD-TYPE 111 119 45
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.94

Table S85.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
BCLAF1 MUTATED 0 2 2 0 1 1
BCLAF1 WILD-TYPE 29 35 62 40 79 31
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
BCLAF1 MUTATED 2 2 2
BCLAF1 WILD-TYPE 114 77 85
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
BCLAF1 MUTATED 1 1 2
BCLAF1 WILD-TYPE 69 73 72
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
BCLAF1 MUTATED 2 2 0
BCLAF1 WILD-TYPE 89 93 32
'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S89.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
PAM MUTATED 1 1 1 0
PAM WILD-TYPE 101 70 47 59
'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.55

Table S90.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
PAM MUTATED 0 0 0 3 0 0
PAM WILD-TYPE 56 42 58 55 26 27
'PAM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0625 (Fisher's exact test), Q value = 0.46

Table S91.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
PAM MUTATED 3 0 0
PAM WILD-TYPE 72 79 55
'PAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
PAM MUTATED 0 1 2 0
PAM WILD-TYPE 39 64 61 42
'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
PAM MUTATED 1 1 1 0 0
PAM WILD-TYPE 31 87 68 31 61
'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
PAM MUTATED 1 2 0
PAM WILD-TYPE 113 119 46
'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.82

Table S95.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
PAM MUTATED 0 0 2 0 0 1
PAM WILD-TYPE 29 37 62 40 80 31
'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.27

Table S96.  Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
PAM MUTATED 0 3 0
PAM WILD-TYPE 116 76 87

Figure S17.  Get High-res Image Gene #10: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.82

Table S97.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
SMARCB1 MUTATED 3 3 0 0
SMARCB1 WILD-TYPE 99 68 48 59
'SMARCB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.23

Table S98.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
SMARCB1 MUTATED 0 4 0 1 1 0
SMARCB1 WILD-TYPE 56 38 58 57 25 27

Figure S18.  Get High-res Image Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SMARCB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
SMARCB1 MUTATED 1 2 1
SMARCB1 WILD-TYPE 74 77 54
'SMARCB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 0.97

Table S100.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
SMARCB1 MUTATED 1 2 0 1
SMARCB1 WILD-TYPE 38 63 63 41
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.55

Table S101.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
SMARCB1 MUTATED 1 0 4 0 1
SMARCB1 WILD-TYPE 31 88 65 31 60
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.6

Table S102.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
SMARCB1 MUTATED 5 1 0
SMARCB1 WILD-TYPE 109 120 46
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.82

Table S103.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
SMARCB1 MUTATED 0 1 0 0 4 1
SMARCB1 WILD-TYPE 29 36 64 40 76 31
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.82

Table S104.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
SMARCB1 MUTATED 3 0 3
SMARCB1 WILD-TYPE 113 79 84
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.38

Table S105.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
SMARCB1 MUTATED 0 0 4
SMARCB1 WILD-TYPE 70 74 70

Figure S19.  Get High-res Image Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.56

Table S106.  Gene #11: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
SMARCB1 MUTATED 0 4 0
SMARCB1 WILD-TYPE 91 91 32
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.91

Table S107.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
KDM6A MUTATED 4 1 1 4
KDM6A WILD-TYPE 98 70 47 55
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0679 (Fisher's exact test), Q value = 0.46

Table S108.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
KDM6A MUTATED 1 4 0 3 0 2
KDM6A WILD-TYPE 55 38 58 55 26 25
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
KDM6A MUTATED 2 3 2
KDM6A WILD-TYPE 73 76 53
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
KDM6A MUTATED 1 1 3 2
KDM6A WILD-TYPE 38 64 60 40
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 0.92

Table S111.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
KDM6A MUTATED 1 2 5 0 2
KDM6A WILD-TYPE 31 86 64 31 59
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.82

Table S112.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
KDM6A MUTATED 6 2 2
KDM6A WILD-TYPE 108 119 44
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0858 (Fisher's exact test), Q value = 0.49

Table S113.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
KDM6A MUTATED 3 3 2 0 1 1
KDM6A WILD-TYPE 26 34 62 40 79 31
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.97

Table S114.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
KDM6A MUTATED 6 2 2
KDM6A WILD-TYPE 110 77 85
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.82

Table S115.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
KDM6A MUTATED 4 1 2
KDM6A WILD-TYPE 66 73 72
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
KDM6A MUTATED 4 3 0
KDM6A WILD-TYPE 87 92 32
'AR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.85

Table S117.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
AR MUTATED 6 4 0 3
AR WILD-TYPE 96 67 48 56
'AR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S118.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
AR MUTATED 1 4 4 2 2 0
AR WILD-TYPE 55 38 54 56 24 27
'AR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
AR MUTATED 3 3 2
AR WILD-TYPE 72 76 53
'AR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S120.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
AR MUTATED 2 2 2 2
AR WILD-TYPE 37 63 61 40
'AR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
AR MUTATED 1 6 3 0 3
AR WILD-TYPE 31 82 66 31 58
'AR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 0.79

Table S122.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
AR MUTATED 7 6 0
AR WILD-TYPE 107 115 46
'AR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
AR MUTATED 1 2 3 4 2 1
AR WILD-TYPE 28 35 61 36 78 31
'AR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
AR MUTATED 7 3 3
AR WILD-TYPE 109 76 84
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
AR MUTATED 3 6 3
AR WILD-TYPE 67 68 71
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'AR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
AR MUTATED 7 4 1
AR WILD-TYPE 84 91 31
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.82

Table S127.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
TP53 MUTATED 3 0 1 3
TP53 WILD-TYPE 99 71 47 56
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0715 (Fisher's exact test), Q value = 0.46

Table S128.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
TP53 MUTATED 1 3 0 0 1 1
TP53 WILD-TYPE 55 39 58 58 25 26
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.82

Table S129.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
TP53 MUTATED 0 1 2
TP53 WILD-TYPE 75 78 53
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S130.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
TP53 MUTATED 0 1 1 1
TP53 WILD-TYPE 39 64 62 41
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.59

Table S131.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
TP53 MUTATED 0 0 3 1 3
TP53 WILD-TYPE 32 88 66 30 58
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.23

Table S132.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
TP53 MUTATED 4 0 3
TP53 WILD-TYPE 110 121 43

Figure S20.  Get High-res Image Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.91

Table S133.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
TP53 MUTATED 1 2 1 2 1 0
TP53 WILD-TYPE 28 35 63 38 79 32
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
TP53 MUTATED 4 1 2
TP53 WILD-TYPE 112 78 85
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.92

Table S135.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
TP53 MUTATED 2 0 2
TP53 WILD-TYPE 68 74 72
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.56

Table S136.  Gene #14: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
TP53 MUTATED 0 4 0
TP53 WILD-TYPE 91 91 32
'KRTAP4-5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S137.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
KRTAP4-5 MUTATED 2 2 1 0
KRTAP4-5 WILD-TYPE 100 69 47 59
'KRTAP4-5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S138.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
KRTAP4-5 MUTATED 1 1 2 0 0 1
KRTAP4-5 WILD-TYPE 55 41 56 58 26 26
'KRTAP4-5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
KRTAP4-5 MUTATED 2 1 1
KRTAP4-5 WILD-TYPE 73 78 54
'KRTAP4-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.82

Table S140.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
KRTAP4-5 MUTATED 2 0 1 1
KRTAP4-5 WILD-TYPE 37 65 62 41
'KRTAP4-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
KRTAP4-5 MUTATED 1 2 1 0 1
KRTAP4-5 WILD-TYPE 31 86 68 31 60
'KRTAP4-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
KRTAP4-5 MUTATED 2 2 1
KRTAP4-5 WILD-TYPE 112 119 45
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.59

Table S143.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
KRTAP4-5 MUTATED 1 2 1 0 0 1
KRTAP4-5 WILD-TYPE 28 35 63 40 80 31
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
KRTAP4-5 MUTATED 3 1 1
KRTAP4-5 WILD-TYPE 113 78 86
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
KRTAP4-5 MUTATED 2 1 1
KRTAP4-5 WILD-TYPE 68 73 73
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 0.85

Table S146.  Gene #15: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
KRTAP4-5 MUTATED 3 1 0
KRTAP4-5 WILD-TYPE 88 94 32
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 0.91

Table S147.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
BRAF MUTATED 3 0 0 1
BRAF WILD-TYPE 99 71 48 58
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S148.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
BRAF MUTATED 2 0 1 0 0 0
BRAF WILD-TYPE 54 42 57 58 26 27
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S149.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
BRAF MUTATED 1 1 1
BRAF WILD-TYPE 74 78 54
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
BRAF MUTATED 1 1 0 1
BRAF WILD-TYPE 38 64 63 41
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
BRAF MUTATED 0 1 2 0 1
BRAF WILD-TYPE 32 87 67 31 60
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
BRAF MUTATED 2 2 0
BRAF WILD-TYPE 112 119 46
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.9

Table S153.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
BRAF MUTATED 1 0 0 1 1 1
BRAF WILD-TYPE 28 37 64 39 79 31
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.92

Table S154.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
BRAF MUTATED 3 0 1
BRAF WILD-TYPE 113 79 86
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.82

Table S155.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
BRAF MUTATED 2 1 0
BRAF WILD-TYPE 68 73 74
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.58

Table S156.  Gene #16: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
BRAF MUTATED 3 0 0
BRAF WILD-TYPE 88 95 32
'KIAA0922 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S157.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
KIAA0922 MUTATED 2 1 0 2
KIAA0922 WILD-TYPE 100 70 48 57
'KIAA0922 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S158.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
KIAA0922 MUTATED 2 1 1 1 0 0
KIAA0922 WILD-TYPE 54 41 57 57 26 27
'KIAA0922 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.82

Table S159.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
KIAA0922 MUTATED 2 2 1 0 0
KIAA0922 WILD-TYPE 30 86 68 31 61
'KIAA0922 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S160.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
KIAA0922 MUTATED 1 3 1
KIAA0922 WILD-TYPE 113 118 45
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
KIAA0922 MUTATED 1 0 2 0 2 0
KIAA0922 WILD-TYPE 28 37 62 40 78 32
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
KIAA0922 MUTATED 1 2 2
KIAA0922 WILD-TYPE 115 77 85
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.55

Table S163.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
KIAA0922 MUTATED 0 0 3
KIAA0922 WILD-TYPE 70 74 71
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.82

Table S164.  Gene #17: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
KIAA0922 MUTATED 0 3 0
KIAA0922 WILD-TYPE 91 92 32
'KRT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0695 (Fisher's exact test), Q value = 0.46

Table S165.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
KRT2 MUTATED 1 4 0 0
KRT2 WILD-TYPE 101 67 48 59
'KRT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S166.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
KRT2 MUTATED 1 1 2 1 0 0
KRT2 WILD-TYPE 55 41 56 57 26 27
'KRT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S167.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
KRT2 MUTATED 2 2 1
KRT2 WILD-TYPE 73 77 54
'KRT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S168.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
KRT2 MUTATED 1 2 1 1
KRT2 WILD-TYPE 38 63 62 41
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S169.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
KRT2 MUTATED 0 2 2 1 0
KRT2 WILD-TYPE 32 86 67 30 61
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S170.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
KRT2 MUTATED 2 2 1
KRT2 WILD-TYPE 112 119 45
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
KRT2 MUTATED 0 1 2 0 1 1
KRT2 WILD-TYPE 29 36 62 40 79 31
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
KRT2 MUTATED 3 1 1
KRT2 WILD-TYPE 113 78 86
'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.82

Table S173.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
KRT2 MUTATED 2 0 1
KRT2 WILD-TYPE 68 74 73
'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 0.97

Table S174.  Gene #18: 'KRT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
KRT2 MUTATED 1 1 1
KRT2 WILD-TYPE 90 94 31
'ALMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.87

Table S175.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
ALMS1 MUTATED 5 1 0 2
ALMS1 WILD-TYPE 97 70 48 57
'ALMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S176.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
ALMS1 MUTATED 2 2 2 1 0 1
ALMS1 WILD-TYPE 54 40 56 57 26 26
'ALMS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S177.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
ALMS1 MUTATED 3 2 2
ALMS1 WILD-TYPE 72 77 53
'ALMS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.82

Table S178.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
ALMS1 MUTATED 0 1 4 2
ALMS1 WILD-TYPE 39 64 59 40
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S179.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
ALMS1 MUTATED 0 3 2 1 2
ALMS1 WILD-TYPE 32 85 67 30 59
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S180.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
ALMS1 MUTATED 3 3 2
ALMS1 WILD-TYPE 111 118 44
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
ALMS1 MUTATED 0 1 1 2 3 1
ALMS1 WILD-TYPE 29 36 63 38 77 31
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
ALMS1 MUTATED 3 2 3
ALMS1 WILD-TYPE 113 77 84
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
ALMS1 MUTATED 2 3 2
ALMS1 WILD-TYPE 68 71 72
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
ALMS1 MUTATED 4 2 1
ALMS1 WILD-TYPE 87 93 31
'GXYLT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.82

Table S185.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
GXYLT1 MUTATED 0 2 1 1
GXYLT1 WILD-TYPE 102 69 47 58
'GXYLT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S186.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
GXYLT1 MUTATED 0 1 1 1 1 0
GXYLT1 WILD-TYPE 56 41 57 57 25 27
'GXYLT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.93

Table S187.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
GXYLT1 MUTATED 0 2 1
GXYLT1 WILD-TYPE 75 77 54
'GXYLT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.92

Table S188.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
GXYLT1 MUTATED 0 2 0 1
GXYLT1 WILD-TYPE 39 63 63 41
'GXYLT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S189.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
GXYLT1 MUTATED 0 2 1 0 1
GXYLT1 WILD-TYPE 32 86 68 31 60
'GXYLT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S190.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
GXYLT1 MUTATED 2 2 0
GXYLT1 WILD-TYPE 112 119 46
'GXYLT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.66

Table S191.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
GXYLT1 MUTATED 0 1 3 0 0 0
GXYLT1 WILD-TYPE 29 36 61 40 80 32
'GXYLT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
GXYLT1 MUTATED 1 2 1
GXYLT1 WILD-TYPE 115 77 86
'GXYLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 0.97

Table S193.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
GXYLT1 MUTATED 1 2 0
GXYLT1 WILD-TYPE 69 72 74
'GXYLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.36

Table S194.  Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
GXYLT1 MUTATED 1 0 2
GXYLT1 WILD-TYPE 90 95 30

Figure S21.  Get High-res Image Gene #20: 'GXYLT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ATP1B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.65

Table S195.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
ATP1B1 MUTATED 3 0 3 1
ATP1B1 WILD-TYPE 99 71 45 58
'ATP1B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S196.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
ATP1B1 MUTATED 2 1 0 1 1 1
ATP1B1 WILD-TYPE 54 41 58 57 25 26
'ATP1B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S197.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
ATP1B1 MUTATED 1 2 2
ATP1B1 WILD-TYPE 74 77 53
'ATP1B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S198.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
ATP1B1 MUTATED 0 1 2 2
ATP1B1 WILD-TYPE 39 64 61 40
'ATP1B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0541 (Fisher's exact test), Q value = 0.45

Table S199.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
ATP1B1 MUTATED 0 0 4 0 3
ATP1B1 WILD-TYPE 32 88 65 31 58
'ATP1B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.66

Table S200.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
ATP1B1 MUTATED 5 1 1
ATP1B1 WILD-TYPE 109 120 45
'ATP1B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S201.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
ATP1B1 MUTATED 1 1 0 3 2 0
ATP1B1 WILD-TYPE 28 36 64 37 78 32
'ATP1B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
ATP1B1 MUTATED 4 1 2
ATP1B1 WILD-TYPE 112 78 85
'ATP1B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.42

Table S203.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
ATP1B1 MUTATED 4 0 1
ATP1B1 WILD-TYPE 66 74 73

Figure S22.  Get High-res Image Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ATP1B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S204.  Gene #21: 'ATP1B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
ATP1B1 MUTATED 2 3 0
ATP1B1 WILD-TYPE 89 92 32
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S205.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
PBRM1 MUTATED 5 2 1 3
PBRM1 WILD-TYPE 97 69 47 56
'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.084

Table S206.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
PBRM1 MUTATED 0 3 2 1 5 0
PBRM1 WILD-TYPE 56 39 56 57 21 27

Figure S23.  Get High-res Image Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.75

Table S207.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
PBRM1 MUTATED 3 2 5
PBRM1 WILD-TYPE 72 77 50
'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.66

Table S208.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
PBRM1 MUTATED 1 2 2 5
PBRM1 WILD-TYPE 38 63 61 37
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0797 (Fisher's exact test), Q value = 0.48

Table S209.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
PBRM1 MUTATED 1 2 7 0 1
PBRM1 WILD-TYPE 31 86 62 31 60
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0732 (Fisher's exact test), Q value = 0.46

Table S210.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
PBRM1 MUTATED 8 3 0
PBRM1 WILD-TYPE 106 118 46
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.4

Table S211.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
PBRM1 MUTATED 1 3 2 4 0 1
PBRM1 WILD-TYPE 28 34 62 36 80 31

Figure S24.  Get High-res Image Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00186 (Fisher's exact test), Q value = 0.081

Table S212.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
PBRM1 MUTATED 10 1 0
PBRM1 WILD-TYPE 106 78 87

Figure S25.  Get High-res Image Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.85

Table S213.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
PBRM1 MUTATED 4 1 3
PBRM1 WILD-TYPE 66 73 71
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.85

Table S214.  Gene #22: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
PBRM1 MUTATED 5 3 0
PBRM1 WILD-TYPE 86 92 32
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S215.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
PTEN MUTATED 2 1 1 2
PTEN WILD-TYPE 100 70 47 57
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.66

Table S216.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
PTEN MUTATED 0 2 1 4 0 0
PTEN WILD-TYPE 56 40 57 54 26 27
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S217.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
PTEN MUTATED 2 3 2
PTEN WILD-TYPE 73 76 53
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S218.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
PTEN MUTATED 2 2 1 2
PTEN WILD-TYPE 37 63 62 40
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S219.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
PTEN MUTATED 1 1 3 1 0
PTEN WILD-TYPE 31 87 66 30 61
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.86

Table S220.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
PTEN MUTATED 1 4 1
PTEN WILD-TYPE 113 117 45
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.82

Table S221.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
PTEN MUTATED 1 3 1 0 2 0
PTEN WILD-TYPE 28 34 63 40 78 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.93

Table S222.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
PTEN MUTATED 3 3 1
PTEN WILD-TYPE 113 76 86
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
PTEN MUTATED 2 2 1
PTEN WILD-TYPE 68 72 73
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.55

Table S224.  Gene #23: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
PTEN MUTATED 4 0 1
PTEN WILD-TYPE 87 95 31
'SAV1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.39

Table S225.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
SAV1 MUTATED 1 0 1 4
SAV1 WILD-TYPE 101 71 47 55

Figure S26.  Get High-res Image Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SAV1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.14

Table S226.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
SAV1 MUTATED 1 0 0 0 1 3
SAV1 WILD-TYPE 55 42 58 58 25 24

Figure S27.  Get High-res Image Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SAV1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.85

Table S227.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
SAV1 MUTATED 3 1 0
SAV1 WILD-TYPE 72 78 55
'SAV1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.85

Table S228.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
SAV1 MUTATED 0 1 3 0
SAV1 WILD-TYPE 39 64 60 42
'SAV1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.025

Table S229.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
SAV1 MUTATED 0 0 0 0 6
SAV1 WILD-TYPE 32 88 69 31 55

Figure S28.  Get High-res Image Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SAV1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.025

Table S230.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
SAV1 MUTATED 1 0 5
SAV1 WILD-TYPE 113 121 41

Figure S29.  Get High-res Image Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SAV1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.82

Table S231.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
SAV1 MUTATED 0 1 1 3 1 0
SAV1 WILD-TYPE 29 36 63 37 79 32
'SAV1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.65

Table S232.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
SAV1 MUTATED 1 4 1
SAV1 WILD-TYPE 115 75 86
'SAV1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.82

Table S233.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
SAV1 MUTATED 0 3 1
SAV1 WILD-TYPE 70 71 73
'SAV1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.85

Table S234.  Gene #24: 'SAV1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
SAV1 MUTATED 3 1 0
SAV1 WILD-TYPE 88 94 32
'CALCR MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S235.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
CALCR MUTATED 1 1 0 1
CALCR WILD-TYPE 101 70 48 58
'CALCR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S236.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
CALCR MUTATED 1 0 2 0 0 0
CALCR WILD-TYPE 55 42 56 58 26 27
'CALCR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S237.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
CALCR MUTATED 2 1 0
CALCR WILD-TYPE 73 78 55
'CALCR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S238.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
CALCR MUTATED 1 1 1 0
CALCR WILD-TYPE 38 64 62 42
'CALCR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.82

Table S239.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
CALCR MUTATED 0 2 0 1 0
CALCR WILD-TYPE 32 86 69 30 61
'CALCR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0711 (Fisher's exact test), Q value = 0.46

Table S240.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
CALCR MUTATED 0 1 2
CALCR WILD-TYPE 114 120 44
'CALCR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
CALCR MUTATED 0 0 0 1 2 0
CALCR WILD-TYPE 29 37 64 39 78 32
'CALCR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 0.93

Table S242.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
CALCR MUTATED 1 0 2
CALCR WILD-TYPE 115 79 85
'CALCR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S243.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
CALCR MUTATED 0 1 2
CALCR WILD-TYPE 70 73 72
'CALCR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S244.  Gene #25: 'CALCR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
CALCR MUTATED 1 2 0
CALCR WILD-TYPE 90 93 32
'IGSF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 0.97

Table S245.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 102 71 48 59
IGSF3 MUTATED 3 1 0 0
IGSF3 WILD-TYPE 99 70 48 59
'IGSF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S246.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 56 42 58 58 26 27
IGSF3 MUTATED 1 2 1 0 0 0
IGSF3 WILD-TYPE 55 40 57 58 26 27
'IGSF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0922 (Fisher's exact test), Q value = 0.51

Table S247.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 75 79 55
IGSF3 MUTATED 0 1 3
IGSF3 WILD-TYPE 75 78 52
'IGSF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.074 (Fisher's exact test), Q value = 0.46

Table S248.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 65 63 42
IGSF3 MUTATED 0 1 0 3
IGSF3 WILD-TYPE 39 64 63 39
'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.85

Table S249.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 88 69 31 61
IGSF3 MUTATED 0 1 3 0 0
IGSF3 WILD-TYPE 32 87 66 31 61
'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.86

Table S250.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 121 46
IGSF3 MUTATED 3 1 0
IGSF3 WILD-TYPE 111 120 46
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.969 (Fisher's exact test), Q value = 1

Table S251.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 29 37 64 40 80 32
IGSF3 MUTATED 0 1 1 1 1 0
IGSF3 WILD-TYPE 29 36 63 39 79 32
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0683 (Fisher's exact test), Q value = 0.46

Table S252.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 79 87
IGSF3 MUTATED 4 0 0
IGSF3 WILD-TYPE 112 79 87
'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.37

Table S253.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 74 74
IGSF3 MUTATED 3 0 0
IGSF3 WILD-TYPE 67 74 74

Figure S30.  Get High-res Image Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S254.  Gene #26: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 91 95 32
IGSF3 MUTATED 1 2 0
IGSF3 WILD-TYPE 90 93 32
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/22574639/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/22542911/KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 282

  • Number of significantly mutated genes = 26

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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